institute for computational biomedicine: Validation Data Set

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[ description ]

This page provides the original data for the Gs pathway and MAPK cascade models generated manually in Kinetikit. They are provided so that users of SigPath can verify that new versions of the software continue to generate valid models for export, or to verify that SigPath interoperates with new modeling environments.

The Gs pathway contains only binding reactions, whereas the MAPK cascade includes mostly enzymatic reactions. Therefore, the validation tests exercise each type of quantitative interaction that SigPath supports in assembling models.

[ documentation ]

In order to run the tests, follow these steps:

The two validation models are already assembled as SPIDs sp218085 (Gs pathway) and sp7 (MAPK cascade).

Go to the page containing the details of that model in the reference version of SigPath (GS: sp218085, MAPK: sp7 ).

Export the model in the format of the modeling environment that you want to test (use the "Export to" buttons in the View Model page).

Load the files generated at step 2 into the modeling environment and run the simulation with the parameters given below.

Compare the concentrations of the molecules used in the figures below (graphs are linked to full-page figures) with the results of the simulation.

GS (sp218085)

Graph of Gs pathway model generated manually in Kinetikit

data from manually generated model in Kinetikit: Gs_pathway.xls

Parameters:
Tmax (maximum time for simulation): 100 sec
dt (integration step): 0.01 sec

MAPK (sp7)

Graph of MAPK cascade model generated manually in Kinetikit

data from manually generated model in Kinetikit: mapk_cascade.xls

Parameters:
Tmax (maximum time for simulation): 200 sec
dt (integration step): 0.01 sec

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Jul 25th, 2005; New SigPath beta release [Release info]
Feb 9th, 2005; New SigPath production release [Release info]
Dec 9-11th, 2004; The First SigPath workshop was held in New York City. [Workshop info]
Nov 3rd, 2004; New SigPath beta release [Release info]
Oct 29th, 2004; New SigPath production released [Release info]
Sep 22nd, 2004; New beta release of SigPath available for preview and testing. [Release info]
Sep 3rd, 2004; A description of SigPath is now available in Science STKE. SigPath users may now cite it as Quantitative information management for the biochemical computation of cellular networks. Campagne F, Neves S, Chang CW, Skrabanek L, Ram PT, Iyengar R, Weinstein H. Science STKE 248:PL11. (2004). [SigPath]
Mar 2nd, 2004; A new release of SigPath is now available. [SigPath]
Mar 1st, 2004; SigPath is now released under the GNU General Public License [download source code]

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